Strain identifier
BacDive ID: 2781
Type strain:
Species: Clostridium autoethanogenum
Strain Designation: JA1-1
Strain history: <- E.-J. Nyns, Catholic University of Louvain, Unit of Bioengineering, Louvain-la Neuve, Belgium; JA1-1
NCBI tax ID(s): 1341692 (strain), 84023 (species)
General
@ref: 3787
BacDive-ID: 2781
DSM-Number: 10061
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Clostridium autoethanogenum JA1-1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from rabbit faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
84023 | species |
1341692 | strain |
strain history
- @ref: 3787
- history: <- E.-J. Nyns, Catholic University of Louvain, Unit of Bioengineering, Louvain-la Neuve, Belgium; JA1-1
doi: 10.13145/bacdive2781.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium autoethanogenum
- full scientific name: Clostridium autoethanogenum Abrini et al. 1994
@ref: 3787
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium autoethanogenum
full scientific name: Clostridium autoethanogenum Abrini et al.
strain designation: JA1-1
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 92.73 | |
69480 | 99.999 | positive |
Culture and growth conditions
culture medium
- @ref: 3787
- name: CLOSTRIDIUM LJUNGDAHLII MEDIUM (DSMZ Medium 879)
- growth: yes
- link: https://mediadive.dsmz.de/medium/879
- composition: Name: CLOSTRIDIUM LJUNGDAHLII MEDIUM (DSMZ Medium 879) Composition: D-Fructose 4.9456 g/l NaHCO3 0.98912 g/l NH4Cl 0.98912 g/l Yeast extract 0.98912 g/l Na2S x 9 H2O 0.296736 g/l L-Cysteine HCl x H2O 0.296736 g/l KH2PO4 0.098912 g/l KCl 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
culture temp
- @ref: 3787
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3787 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 99.631 |
Isolation, sampling and environmental information
isolation
- @ref: 3787
- sample type: rabbit faeces
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Leporidae (Rabbit/Hare) |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_1289.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_42;96_749;97_872;98_1018;99_1289&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: Y18178
- Sequence Identity:
- Total samples: 18602
- soil counts: 2899
- aquatic counts: 1409
- animal counts: 13922
- plant counts: 372
Sequence information
16S sequences
- @ref: 3787
- description: Clostridium autoethanogenum 16S rRNA gene, partial, strain DSM 10061
- accession: Y18178
- length: 1460
- database: ena
- NCBI tax ID: 1341692
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium autoethanogenum DSM 10061 | GCA_001484725 | complete | ncbi | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | GCA_000484505 | complete | ncbi | 1341692 |
66792 | Clostridium autoethanogenum JA1-1 | GCA_002189005 | scaffold | ncbi | 84023 |
66792 | Clostridium autoethanogenum DSM 10061 | GCA_000427255 | contig | ncbi | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | 1341692.11 | complete | patric | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | 1341692.10 | complete | patric | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | 1341692.4 | complete | patric | 1341692 |
66792 | Clostridium autoethanogenum strain JA1-1 | 84023.6 | wgs | patric | 84023 |
66792 | Clostridium autoethanogenum DSM 10061 | 2814123208 | complete | img | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | 2554235459 | complete | img | 1341692 |
66792 | Clostridium autoethanogenum DSM 10061 | 2554235205 | draft | img | 1341692 |
GC content
@ref | GC-content | method |
---|---|---|
3787 | 25.9 | thermal denaturation, midpoint method (Tm) |
3787 | 31.1 | sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 59.067 | no |
gram-positive | yes | 59.596 | no |
anaerobic | yes | 98.559 | yes |
aerobic | no | 97.844 | yes |
halophile | no | 92.411 | no |
spore-forming | yes | 92.464 | no |
glucose-util | yes | 82.903 | no |
motile | yes | 85.394 | no |
thermophile | no | 98.886 | no |
glucose-ferment | yes | 55.804 | no |
External links
@ref: 3787
culture collection no.: DSM 10061
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Metabolism | 23789275 | [Comparison of microorganisms fermenting syngas into ethanol]. | Song A, Feng X, Wang F, Xie H, Yang D | Sheng Wu Gong Cheng Xue Bao | 2013 | Bacteria/classification/*metabolism, Clostridium acetobutylicum/metabolism, Ethanol/isolation & purification/*metabolism, *Fermentation, Gases/*metabolism, Hydrogen/metabolism | Phylogeny | |
Genetics | 23950130 | Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide. | Bruno-Barcena JM, Chinn MS, Grunden AM | Genome Announc | 2013 | 10.1128/genomeA.00628-13 | ||
24655715 | Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. | Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Kopke M | Biotechnol Biofuels | 2014 | 10.1186/1754-6834-7-40 | |||
Metabolism | 26331212 | Traits of selected Clostridium strains for syngas fermentation to ethanol. | Martin ME, Richter H, Saha S, Angenent LT | Biotechnol Bioeng | 2015 | Anaerobiosis, *Biofuels, Biotransformation, Carbon Monoxide/*metabolism, Clostridium/genetics/*metabolism, Ethanol/*metabolism, Fermentation, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Metabolic Networks and Pathways/genetics | 10.1002/bit.25827 | |
Genetics | 26692227 | Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. | Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesman A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP | BMC Genomics | 2015 | Clostridium/*genetics, Data Curation/methods, *Genome, Bacterial, High-Throughput Nucleotide Sequencing/methods, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Sequence Analysis, DNA/*methods | Transcriptome | 10.1186/s12864-015-2287-5 |
Biotechnology | 36032736 | Clostridium autoethanogenum isopropanol production via native plasmid pCA replicon. | Nogle R, Nagaraju S, Utturkar SM, Giannone RJ, Reynoso V, Leang C, Hettich RL, Mitchell WP, Simpson SD, Jewett MC, Kopke M, Brown SD | Front Bioeng Biotechnol | 2022 | 10.3389/fbioe.2022.932363 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3787 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10061) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10061 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 |